WINDHOEK, Namibia (Reuters) -- Russia wants its Central Asian allies to cooperate with Washington on Afghanistan and is ready to work with the United States on a new nuclear arms cuts pact, President Dmitry Medvedev said on June 25.

Afghanistan, viewed by the U.S. as a top foreign policy priority, and a replacement for the expiring 1991 START pact will be at the centre of talks between Medvedev and U.S. President Barack Obama in Moscow next month.

The two issues are also at the heart of attempts by Medvedev and Obama to "reset" ties, which have reached post-Cold War lows under the previous U.S. administration.

Russia has pledged to let the transit of vital non-lethal goods for U.S.-led forces in Afghanistan through its territory. But in February it sent a confusing signal by encouraging a Central Asian ally, Kyrgyzstan, to shut the U.S. Manas air base.

Earlier this week, Kyrgyzstan allowed the United States back to Manas triggering media speculation Russia would be angered, but Medvedev said he saw nothing wrong in the decision.

"We are helping them [Americans], ... and Kyrgyzstan is ready to help," Medvedev told reporters in the Namibian capital Windhoek where he is on a visit. "They are welcome."

Medvedev said he has discussed the return of the U.S. military to Manas with Kyrgyz President Kurmanbek Bakiyev.

Bakiyev ordered Manas shut after securing $2 billion in aid from Russia, though Moscow denies any role in his decision.

Analysts say the Kremlin is concerned by increased U.S. diplomatic activity in Central Asia, Moscow's traditional sphere of interests. Russia has its own air base in Kyrgyzstan.

Medvedev said Russia was happy with the terms of the new deal under which Washington agreed to pay $180 million for the use of Manas to refuel U.S. aircraft bound for Afghanistan.

"[The deal] envisages that the military base ceases to exist, while new transit activities will be run on a different basis, without any immunity for the U.S. military, without much U.S. military personnel," he said.

Medvedev denied suggestions Washington and Moscow were at loggerheads over a new nuclear arms deal to replace START-1, which expires on December 5.

"So far no-one closed doors," Medvedev said in Windhoek. "We continue talking about this with our U.S. partners ahead of the visit by my colleague Barack Obama including on linking anti-missile defence and limiting strategic weapons."

Both leaders see further arms cuts as a key to maintaining global strategic stability.

However, Moscow views U.S. plans to create own antimissile system and deploy elements in Eastern Europe as a threat to its security. And, Medvedev has expressed hopes Obama will be less committed to the missile defence plan than Bush.

Russian media have quoted U.S. officials as rejecting any linkage between the new arms deal and the missile defence.